clipnet/pyproject.toml at main · Danko-Lab/clipnet · GitHub

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[build-system]
requires = ["setuptools>=42"]
build-backend = "setuptools.build_meta"

[project]
name = "clipnet"
version = "0.2.1"
description = """
CLIPNET (Convolutionally Learned, Initiation-Predicting NETwork) is an
ensembled convolutional neural network that predicts transcription
initiation from DNA sequence at single nucleotide resolution. This package
contains code for training, predicting, and interpreting CLIPNET models.
"""
authors = [{ name = "Adam He", email = "adamyhe@gmail.com" }]
license = { file = "LICENSE" }
urls = { homepage = "https://github.com/adamyhe/clipnet" }
requires-python = "~= 3.9"
dependencies = [
    "gputil",
    "h5py",
    "joblib>=1.3",
    "matplotlib",
    "numpy>=1.26.3, <2.0.0",
    "pandas",
    "pyfastx>=1.1",
    "scipy",
    "seqlogo",
    "shap==0.44.1",
    "tensorflow[and-cuda]>=2.14.0, <2.15.0",
    "silence_tensorflow",
    "tqdm>=4.64.1",
]

# Maybe needed?
#biopython
#cmake
#cython
#ghostscript
#pyarrow
#pysam~=0.21.0

[tool.setuptools]
packages = ["clipnet"]

[project.scripts]
clipnet = "clipnet.cli:cli"

[tool.setuptools.package-data]
clipnet = ["data/data_fold_assignments.csv", "data/test.fa"]